Automatic Generation of Reports

Description

Sweave provides a flexible framework for mixing text and R/S code
for automatic report generation. The basic idea is to replace the
code with its output, such that the final document only contains the
text and the output of the statistical analysis: however, the source
code can also be included.

Usage

Arguments

Path to Sweave source file. Note that this can be
supplied without the extension, but the function will only proceed
if there is exactly one Sweave file in the directory whose
basename matches file.

driver

the actual workhorse, (a function returning) a named
list of five functions, see ‘Details’ or the
Sweave manual vignette.

syntax

NULL or an object of class SweaveSyntax or
a character string with its name.
See the section ‘Syntax Definition’.

encoding

The default encoding to assume for file.

...

further arguments passed to the driver's setup function:
see section ‘Details’, or specifically the arguments of the
R...Setup() function in RweaveLatex and
Rtangle, respectively.

Details

Automatic generation of reports by mixing word processing markup (like
latex) and S code. The S code gets replaced by its output (text or
graphs) in the final markup file. This allows a report to be re-generated
if the input data change and documents the code to reproduce the
analysis in the same file that also produces the report.

Sweave combines the documentation and code chunks together (or
their output) into a single document. Stangle extracts only
the code from the Sweave file creating an S source file that can be
run using source. (Code inside \Sexpr{}
statements is ignored by Stangle.)

Stangle is just a wrapper to Sweave specifying a
different default driver. Alternative drivers can be used: the former
CRAN package cacheSweave and the Bioconductor package
weaver provide drivers based on the default driver
RweaveLatex which incorporate ideas of caching
the results of computations on code chunks.

Environment variable SWEAVE_OPTIONS can be used to override the
initial options set by the driver: it should be a comma-separated set
of key=value items, as would be used in a \SweaveOpts
statement in a document.

Non-ASCII source files must contain a line of the form

\usepackage[foo]{inputenc}

(where foo is typically latin1, latin2, utf8 or
cp1252 or cp1250) or they will give an error.
Re-encoding can be turned off completely with argument
encoding = "bytes".

Syntax Definition

Sweave allows a flexible syntax framework for marking
documentation and text chunks. The default is a noweb-style syntax, as
alternative a latex-style syntax can be used. (See the user manual for
further details.)

If syntax = NULL (the default) then the available syntax
objects are consulted in turn, and selected if their extension
component matches (as a regexp) the file name. Objects
SweaveSyntaxNoweb (with extension = "[.][rsRS]nw$") and
SweaveSyntaxLatex (with extension = "[.][rsRS]tex$") are
supplied, but users or packages can supply others with names matching
the pattern SweaveSyntax.*.